He was indoctrinated with Catholic beliefs and superstitions. I see no good reason to believe he didn't continue to harbor those beliefs. Indeed, I would not be surprised if he genuinely thought he was doing God's work.
I can see, however, why Christians, particularly Catholics, would want to distance themselves from him. Still, his genocide was biblical when you look at mythical sources like the book of 1 Samuel. Those poor Amelekites. Psychologically, it would seem that he really did think he was doing God's work.